From my short experience with them before the roll back, the Civvy GB had more armor and was a bit better on energy and firing archs... I think. But the Borderworlds GS was a smaller target and more agile. Both were pretty decent, depends on what you want. Someone correct me if I'm wrong.
BW gunship just seems like a big, slow gunboat with the powercore and armor of a light gunship. It isn't any more agile than a heavy gunboat to coincide with its lighter 'weight'.